The only way I can see it getting solved is the OS sandboxing everything behind the scenes, redirecting everything the application spews in random locations to

The only way I can see it getting solved is the OS sandboxing everything behind the scenes, redirecting everything the application spews in random locations to The One True Profile Folder per application. Even then it wouldn't be without challenges, off the top of my head some method if you actually wanted an application to get out of its sandbox and look at the real documents folder, another method for App1 to look at files in App2's sandbox (and detecting when this is desired), or what to do if an application is able to change how it identifies itself to the OS (new versions?).